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- PDB-9f8w: Crystal structure of the apo Pex5 peroxisomal cargo receptor from... -

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Basic information

Entry
Database: PDB / ID: 9f8w
TitleCrystal structure of the apo Pex5 peroxisomal cargo receptor from Trypanosoma brucei
ComponentsPeroxisome targeting signal 1 receptor PEX5
KeywordsPEPTIDE BINDING PROTEIN / Trypanosoma / Peroxin / Peroxin targeting signal
Function / homology
Function and homology information


peroxisome / metal ion binding
Similarity search - Function
PEX5/PEX5L / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Peroxisome targeting signal 1 receptor PEX5
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBanasik, M.K. / Dubin, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/M/NZ1/00797 Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural dynamics of the TPR domain of the peroxisomal cargo receptor Pex5 in Trypanosoma.
Authors: Banasik, M. / Napolitano, V. / Blat, A. / Abdulkarim, K. / Plewka, J. / Czaplewski, C. / Gieldon, A. / Kozak, M. / Wladyka, B. / Popowicz, G. / Dubin, G.
History
DepositionMay 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome targeting signal 1 receptor PEX5
B: Peroxisome targeting signal 1 receptor PEX5


Theoretical massNumber of molelcules
Total (without water)77,8392
Polymers77,8392
Non-polymers00
Water2,018112
1
A: Peroxisome targeting signal 1 receptor PEX5


Theoretical massNumber of molelcules
Total (without water)38,9201
Polymers38,9201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome targeting signal 1 receptor PEX5


Theoretical massNumber of molelcules
Total (without water)38,9201
Polymers38,9201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.545, 206.545, 67.867
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Peroxisome targeting signal 1 receptor PEX5


Mass: 38919.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pET24a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9U7C3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.9 M sodium-potassium tartrate tetrahydrate, 20% w/v glycerol, 0.05 M Hepes pH 7.4 after 8 days at 293 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.35→47.89 Å / Num. obs: 44917 / % possible obs: 99.89 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 14.68
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 6 % / Num. unique obs: 4490 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→47.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.285 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24605 2307 5.1 %RANDOM
Rwork0.19777 ---
obs0.20025 42612 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.254 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å2-0 Å2
2--0.53 Å2-0 Å2
3----1.71 Å2
Refinement stepCycle: 1 / Resolution: 2.35→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 0 0 112 4935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134962
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174550
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.6376753
X-RAY DIFFRACTIONr_angle_other_deg1.3491.5710401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30923.54274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.29915766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4941529
X-RAY DIFFRACTIONr_chiral_restr0.0740.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021179
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6725.7262530
X-RAY DIFFRACTIONr_mcbond_other4.6715.7242529
X-RAY DIFFRACTIONr_mcangle_it6.6558.5713157
X-RAY DIFFRACTIONr_mcangle_other6.6548.5743158
X-RAY DIFFRACTIONr_scbond_it4.9936.042432
X-RAY DIFFRACTIONr_scbond_other4.9926.0422433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3848.9153593
X-RAY DIFFRACTIONr_long_range_B_refined9.20866.745549
X-RAY DIFFRACTIONr_long_range_B_other9.21566.7435539
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 170 -
Rwork0.317 3136 -
obs--99.97 %

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